The efficiency and accuracy of methods of identifying and quantifying pathogens in samples, such as environmental samples, can be affected by a number of factors. For example, the efficiency of extracting nucleic acids from a sample may vary depending on the characteristics of the sample or the presence of inhibitors in the sample, or depending upon whether samples are subjected to pretreatment steps prior to extracting the nucleic acids. The detection of nucleic acid sequences in a sample can also be affected by a number of factors, such as nucleotide composition or the concentration of nucleic acids in a sample.